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Tytuł pozycji:

GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs.

Tytuł:
GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs.
Autorzy:
Eggertsson HP; deCODE genetics/Amgen Inc., Sturlugata 8, Reykjavik, Iceland. .; School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland. .
Kristmundsdottir S; deCODE genetics/Amgen Inc., Sturlugata 8, Reykjavik, Iceland.; School of Science and Engineering, Reykjavik University, Reykjavik, Iceland.
Beyter D; deCODE genetics/Amgen Inc., Sturlugata 8, Reykjavik, Iceland.
Jonsson H; deCODE genetics/Amgen Inc., Sturlugata 8, Reykjavik, Iceland.
Skuladottir A; deCODE genetics/Amgen Inc., Sturlugata 8, Reykjavik, Iceland.
Hardarson MT; deCODE genetics/Amgen Inc., Sturlugata 8, Reykjavik, Iceland.
Gudbjartsson DF; deCODE genetics/Amgen Inc., Sturlugata 8, Reykjavik, Iceland.; School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland.
Stefansson K; deCODE genetics/Amgen Inc., Sturlugata 8, Reykjavik, Iceland.; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
Halldorsson BV; deCODE genetics/Amgen Inc., Sturlugata 8, Reykjavik, Iceland. .; School of Science and Engineering, Reykjavik University, Reykjavik, Iceland. .
Melsted P; deCODE genetics/Amgen Inc., Sturlugata 8, Reykjavik, Iceland. .; School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland. .
Źródło:
Nature communications [Nat Commun] 2019 Nov 27; Vol. 10 (1), pp. 5402. Date of Electronic Publication: 2019 Nov 27.
Typ publikacji:
Journal Article
Język:
English
Imprint Name(s):
Original Publication: [London] : Nature Pub. Group
MeSH Terms:
Genome, Human*
Genomic Structural Variation*
Software*
Genotyping Techniques/*methods
Computer Graphics ; Databases, Genetic ; Genetics, Population ; Genotyping Techniques/statistics & numerical data ; Humans ; Iceland ; Pedigree ; Polymorphism, Single Nucleotide ; Reproducibility of Results ; Workflow
References:
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Entry Date(s):
Date Created: 20191129 Date Completed: 20200323 Latest Revision: 20231020
Update Code:
20240104
PubMed Central ID:
PMC6881350
DOI:
10.1038/s41467-019-13341-9
PMID:
31776332
Czasopismo naukowe
Analysis of sequence diversity in the human genome is fundamental for genetic studies. Structural variants (SVs) are frequently omitted in sequence analysis studies, although each has a relatively large impact on the genome. Here, we present GraphTyper2, which uses pangenome graphs to genotype SVs and small variants using short-reads. Comparison to the syndip benchmark dataset shows that our SV genotyping is sensitive and variant segregation in families demonstrates the accuracy of our approach. We demonstrate that incorporating public assembly data into our pipeline greatly improves sensitivity, particularly for large insertions. We validate 6,812 SVs on average per genome using long-read data of 41 Icelanders. We show that GraphTyper2 can simultaneously genotype tens of thousands of whole-genomes by characterizing 60 million small variants and half a million SVs in 49,962 Icelanders, including 80 thousand SVs with high-confidence.

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